It is just a case of speaking truth, but in a blunt way.
First of all, none of us were at the pitch, but Shoaib was.
This man is is a bowler, and not a speaker, so we cannot expect him to be very eloquent with his words. He might have noticed hesitation on part of Sachin, and that can easily be taken as "one's being wary" of the fast ball. And one's being wary can often be expressed with the term "dar gaya" in India as well as in Pakistan, and especially in sports.
But the term "scared" or "dar gaya" can mean so many things in so many ways. It is not as if Sachin was scared of Shoaib, but yeah, Sachin must surely have been more careful, wary, and some times pretty hesitant in facing his ball. In describing such mannerism, Shoaib has not been incorrect in spelling it out as "dar gaya".
Because he has also questioned the character of so many other cricketers from Pakistan, it is very obvious they will use the Sachin platform to defend themselves, since everyone knows Sachin has a very strong fan base on both sides of the border, and all his die hard fans are too biased to listen to anything critical of Sachin at all.
Also, only Sachin and Shoaib would know the truth whether whatever Shoaib is speaking is true or not, it is very much possible that Sachin was never hesitant (though I have myself seen him like that, but I am no expert on cricket), but chances are greater that Sachin might have actually been very wary of Shoaib because Shoaib is notorious for continuously bowling really fast balls.
Then comes the match winning part, which Sachin fans would never listen to. But if we give a very close look to the data on Sachin's performance, with respect to the wins he got, Shoaib's allegations appear well founded. Then add to that the previous allegations of Ganguly who openly alleged that Sachin never played for the country, but always for himself. I think Shoaib's taking note of Sachin's pattern is not coincidental, a lot of people did and came to the same conclusion.
Finally BCCI asking Shoaib Akhtar to apologize - Who the heck is BCCI to ask someone to apologize? Shoaib is retired, and BCCI has absolutely no business in whatever he does with his life. Tendulkar has a great sway in BCCI, and we can see where it is coming from, but they forget that dictating someone out of their purview will do nothing more than make them look like a fool.
It is just the case of losing your head when in power.